The North Shore-Long Island Jewish Research Institute is a nationally recognized, growing university-affiliated biomedical and clinical research center with currently 55 NIH funded research grants. Although covering a wide area of biomedical research, the NS-LIJ RI has certain core areas, which serve to focus and to integrate basic and clinical researchers in their elucidation of the bimolecular and clinical pathogenesis of disease states. The NS-LIJ RI has reached a critical mass of scientists who have a well-defined and compelling need to move into the area of proteomics, which requires the powerful analytic capabilities that are realized with LC/MS. The proposed LC/MS instrument is the DECAP-5100 PROTEOMEX INTEGRATED WORKSTATION BUNDLE/LCQ DeeaXP quadrupole ion-trap mass spectrometer with Surveyor HPLC from ThermoFinnigan. It is a fully integrated multidimensional LC/MS system that has been designed and optimized for analysis of complex peptide and protein samples and is also well suited for ICAT (isotope-coded affinity tag) peptide quantitation. This proposed LC/MS system is actually a basic state of the art instrument in the field of proteomic analysis. It couples a multidimensional HPLC, which allows enormous improvement over 2D-PAGE in resolution, sample recovery, mass range and solubility analysis of protein fractions, to an ion trap mass spectrometer with unsurpassed specifications for MS and MS n applications. In addition to the projected main usage in proteomic analysis, the instrument will also be capable of small molecule quantitation and structural elucidation for drug metabolism and drug discovery studies. The Instrument will be integrated into the Institute's Core Facility with a dedicated mass spec operator and technical guidance with the two Ph.D. scientists in charge. The instrument we have requested will allow the investigators to attain the goals described within their NIH funded research projects and more including: high throughput analysis of antigenic peptide repertoires, identification and quantitation of small molecule condensation and metabolic break down products. In order for science at the Institute to continue at a competitive pace and for our investigators to expand their research capabilities and horizons, we need to establish a shared mass spectrometer resource.